Operation Repopulation
by IfUKnewUCouldNotFail
Summary: They finally have the cure…but are they in time to save the world? Or will more drastic measures need to be taken to safeguard the survival of the human race… Starts just after the episode 'Trials' ends and continues on to 'No Place Like Home…' and beyond. Tom/Rachel.
1. Chapter 1

Disclaimer: Don't own Last Ship.

A/N: Believe it or not, this was actually the first fic I started for this fandom, but after stalling on it I moved ahead and concentrated on some other writings that my muse held preference for at the time. I recently decided to come back to it and have made enough progress to post the first chapter for you. I hope you like it and let me know what you think and if you think it has potential to continue. At this stage I am not sure of the exact direction I am taking this fic…though more because of having too many different ideas, as opposed to too few… ;-)

LSLSLS

"Captain, may I have a moment please?" She spoke quickly, the moment he opened the door to his office/cabin, answering her hail. Her words seemed a little formal even to her, especially considering they had been knee deep in a long tight celebratory not-entirely-platonic-if-she-was-honest-with-herself embrace a mere few hours ago.

With a tilt of his head and slight look of curiosity in his handsome features, he acquiesced and allowed her entry to his cabin, resealing the entryway behind them. His lack of a verbal greeting made Rachel think he had caught on to her slightly too formal tone and was now a little on edge waiting for what she had to say. She didn't expect his first words, though she should have of course. But her mind having basically solved one massive problem that had been heavily occupying it for months, had run at rocket speed to start solving the next one on the list…granted, the next problem had been elevated several spaces on that list by two Navy Lieutenants that were currently resting in her no longer actively quarantined lab.

"Are they ok? Has anything happened? They all seemed fine when I left…otherwise I wouldn't have…" she stopped him there.

"No, no, Captain! They are all fine, better than fine…given the givens. Improving at a rate greater than the most optimistic estimates I could have possibly predicted…it's amazing really." She smiled as she thought of the lives that so easily could have been extinguished that day, but had survived and because of that the human race now had a chance to survive too.

Captain Chandler relaxed slightly at that, an ever so slight smirk marring his features now. He knew that to anyone else's ears, she was just stroking her own ego, praising her own work like that.

But he knew her better, even after these few short months. Hell, even in a single month, because he was the one that had so specifically pointed out that she had barely said more than a few words to him for the preceding four months that she had first been on his ship, just before everything had gone completely FUBAR.

He wondered if Tophet really knew her at all, despite their many years of working together. After overhearing their very heated argument when Rachel had needed her former assistant's help back in the lab after he had betrayed them all…it was kind of impossible not to, they were _very _loud…he now had to come to the conclusion that the other man didn't really know her at all. Of course it was also possible that the man had been so deep in anger, recrimination and grief that he had just been saying anything that popped into his head to lash out and try and hurt her.

He had accused her of loving the situation they had been in, the whole world dependent on her to save it. He had also made some rather harsh comments about her love life…or for accurately…her sex life. Basically saying that the global pandemic made no never mind to her as she was basically alone and had no-one and nothing to lose.

Tom didn't think either remark could be further from the truth. In both casing he had accused her of not caring and not feeling, and the woman he had come to know cared and felt deeply…she just hid it well…clearly having already experienced the pain of loss in her life. At least it was clear to him. And even if parts of what the man had said had some truth to them, was being all alone for the end of the world really a situation to be envied?

Rachel's voice drew Tom back from his internal musings. "As you know I broke the quarantine as it was no longer needed, not only are they all free of the virus, they are all now immune to it." They both smiled at that.

"After you left I let Tex, Andrea, Miller and the Master Chief retire to their own quarters. We'll continue to keep an eye on them, but what they most need right now is rest. "

"But not Lt. Foster?"

"She needs rest of course and like I said she is recovering extremely well, but in her case I would like her to stay more closely monitored… at least till morning."

Tom raised an eyebrow. Rachel could see he wanted more. She gave in.

"If her condition is going to be…negatively impacted…due to the stress of what she has just gone through…it is likely to happen sooner rather than later."

Tom understood perfectly what she was saying.

"Do you think that is likely?"

"At the moment all indications are good. I think she has already past the largest part of the danger…but I will be a lot happier when she makes it through the night uneventfully. Keeping a closer eye on her during the time till then is just a wise precaution."

Tom dipped his head in acceptance of statement. Seeming to think that particular line of conversation was done for now. He took a seat and indicted for Rachel to do the same, she did.

As soon as he sat, his eyes closed and his head leaned back briefly with lethargy. It suddenly looked like all the exhaustion, that adrenaline and sheer force of will had been holding back the last few days, had crashed back upon him in an instant.

Rachel was somehow pleased that he felt comfortable enough around her to let even this small show of weakness occur in her presence, so rare was it that he let any part of his always fully in control military persona slip. Another part of her recognized how tired he really must be to let even her see it and thought that maybe this wasn't the best time to bring this subject up. She considered it for only a moment before realizing there was no choice; it had to be now, before he could take any contrary measures to the ones she was going to advocate.

"Captain…Tom…" That got his attention, the use of his first name. Somehow, as much as this was the professional conversation of a scientist with something important to convey to a leader…it also had a deeply personal nature to it…at least to her.

There were some very obvious and _very personal_ implications…at least for her.

She also hoped that her fledgling friend Tom might be more willing to listen to his new friend Rachel than Captain Chandler might be to listen to an annoying scientist making what was going to seem like some extreme proposals.

She went on. "…I need to talk to you about something else…well, it is actually rather stronger connected to the situation with Lieutenant's Foster and Green. Which is why it has to be now, I know how tired you must be…both of us…but I need to say this before you take any action in their case."

"And just what action do you think I'm going to take?"

"Come on, Tom. Don't play coy with me. Frankly, I don't know what action you plan on taking, considering that all your usual avenues of recourse are firmly closed. I would hazard a guess that you don't have a clue what you can do at this point either, but what I do know is every military bone in your body is probably calling for you to find a way to _heavily discourage_ this type of thing from ever happening again."

"And what's wrong with that?"

"_Everything_ is wrong with that, Captain!"

He eyed more closely at her small but uncharacteristic outburst…sure, she was tired an emotionally drained…they both were, but this was a level of passion she usually reserved for saving the world… She must find this topic of conversation extremely important.

"Explain." He spoke calmly, his full attention on her; letting her know he was aware of the ardor she felt for this subject and would respect her enough to hear her out…even though he couldn't hazard a guess as to where she was heading with this that was so _very_ important.

Rachel sighed, relieved; he was willing to listen to her…that was a victory in itself…she could only hope he was still willing to listen to her after she has made her seemingly wild but unfortunately accurate contentions.

"Because the world has been turned on his head, Captain, and this no-fraternizing, a battle ship is no place for pregnant woman and children idea has been turned on its head with it."

"How do you figure that?"

"Tom" She went back to her use of his first name, it seemed right, she really needed him to listen to her on this, to trust her. "…I understand you well enough to know the way you're thinking in a crisis like this, hell, how any _good_ military leader in your position would be thinking. You were all trained on how to deal with crises, and I have witnessed how much of that training has served you and everyone on this ship very well…for the most part."

"For the most part?" Tom knew he was going to have to start coming up with responses that consisted of more than a couple of words soon. It just wasn't easy as he literally had no idea where she was heading with this yet…he had an uneasy feeling though…especially if she was suggested doing away with any of the rules that had been drummed into him is whole career as practically being the word of God…which it very much seemed she was.

"My point is, that while I'm sure you were trained for a large variety of different crises, I'm also fairly sure you were never trained for a crisis of this immense magnitude. The very survival of the human species is hanging in a very fragile balance and very much dependent on the decisions our few remaining leaders make. Tell me, did they have a class on procedures for rebuilding civilization after the apocalypse at the academy…?" She let the question hang meaningfully, before continuing on.

"What I'm sure they did teach you, basic principle that it is, is that when the situation changes, the protocol for handling that situation must change too. Take Lt. Foster's situation, in normal circumstances; aside from any other action to be taken she would be transferred off this ship so fast her head would be spinning. Now aside from that being a clear part of her punishment…and don't even try denying it…" She added when he went to interrupt. Tom shut his mouth again...eventually…making the choice to continue to listen patiently…with some effort.

"As I was saying…aside from that being a part of her punishment, it would also be because a battleship is not a place for a pregnant woman or a baby, now why is that?"

"Because it's not safe." Was his automatic response.

"Exactly! But the truth is it _wasn't _safe, past tense. Safety is a relative condition. All it really means is the more safe option, as true complete safety is not something that actually exists. I think the fact that the very notion of removing Kara from this ship, has not even come up, proves that you already know that this is the safest place for her."

"I'll give you that, and I don't have any intention of kicking either Foster or Green off the ship, _or_ doing very much in the way of punishing either of them, especially given we have already been there. But that doesn't mean this kind of thing needs to be encouraged to happen again."

"On the contrary Captain, _encouraged_ is exactly what it needs to be. Our population is decimated…and it is unfortunately going to be further decimated before this virus is eliminated. The outcome of these trials was better than I could possibly have expected, the tragic loss of one of our people obviously not withstanding." She finished on a dejected whispered breath, eyes lowered, remembering the girl whose death he knows he can't prevent her for forever blaming herself for…

He understood…he blamed himself too, and he didn't miss the way she said 'one of _our _people' either. Only mere weeks ago, it would have been 'one of _your_ people' such was the outsider she was considered by the crew at large and indeed how she had considered herself back then. He brought his attention back to focus solely on her as he watched her take a long deep breath, seemingly drawing strength from internal reserves he couldn't believe still existed, before continuing.

"The problem is, even if we somehow achieved the impossible and made the entirety of what's left the world's population immune to the virus tomorrow, the human race would still be at severe risk of extinction the day after that."

She paused to let the enormity of her statement sink in for full effect.

He didn't know what to say to that, everything about their every waking moment of the last month had been about creating a vaccine for the virus and saving the world. Somehow, until now he had considered those two things the same, not letting himself think about what came next.

"Captain…people are dying virtually every second…. our population is dwindling…at a rate that is beyond alarming. You and I both know that even with not only a vaccine, but now a cure, we are not going to be able to save everybody tomorrow, not even next week…probably not even next month. And millions more are going to continue to die in that time, and what's more than that, the death toll from this crisis is not going to stop when everybody still alive receives the vaccine."

"You don't think it will work on everybody?" He mistook her words.

"No, I have every confidence that the cure will be very effective, provided a patient isn't too far gone. That is not what I am saying here, my concerns over continuing fatalities…continuing decline in population… is related to the difficulties and set backs we are likely to encounter in mass-producing and disseminating the cure _and_ the following fallout of a world that has been plunged into post apocalypse survival mode. And that's not even mentioning the various other deadly diseases which invariably pop out the woodwork after such large scale disasters…I can assure you a plague that kills billions of people is not going to be the exception to that rule…"

Tom continued to watch and listen on as, barely taking a breath, she continued.

"Your instinct and the instinct of the whole world that have previously, for the most part, existed in the modern era is going to be to wait until things settle down, until things are safer and back to normal before looking at repopulating. It is a natural instinct to want to raise our children in an environment that is as safe as possible, but in this extreme circumstance, that instinct is _wrong_. The certainty that I am trying to convey to you here is that none of those things are going to happen in the near future…not even in our lifetime probably. Too many and too much of who and what we were has been destroyed. Things are not going to become settled, safe or normal for a very long time and if we wait for them to...it will never happen because the human race **_will have died out_**."

TBC

A/N: Reviews make me smile. :-)


	2. Chapter 2

Here they were again, back in his office…alone…again. Tom had taken a seat perched on his office stool, spun around to face Rachel where she had slumped down on his couch upon entering the cabin with him. For all the world she looked like she was struggling to support a weight as great as the world on her shoulders. As he studied her distant eyes staring off into space…he supposed she was. It was a weight he sorely wished he had the power to unburden her of.

The last time they had been here, just before Baltimore, when she had personally given him the cure she had created, had been a time filled with so much hope…now that hope was all but dashed.

The time before that, had been just after the trials…that had been an infinitely more hopefully occasion too…even with the loss they suffered.

It had been on that occasion that Rachel had chosen…with the help of two of his Lieutenants…to voice her populace concerns to him…and her recommendations for taking action against those concerns. They had not been recommendations that he had been particularly willing to hear…then.

But so much had gone down in the interim since there last moments spent alone in this room. So much had changed...gotten worse…from a situation it had been almost impossible to imagine how it could get worse.

Discoveries of the atrocities of Baltimore obviously weighed heavily on him too. How could they not? His own children and father had been mere moments away from falling victim too them as well, but he had finally and thankfully found them in time…many, many others had not been so fortunate.

But what was impossible to remove from the forefront of his mind, despite all their other losses and unfortunate realizations, was that he had lost Darien. He had lost his wife to this plague. It was for sure now, not just the possible occurrence he had worried about…it had happened. He had lost his wife and his children had lost their Mother.

But that was the thing right there. He still had his children…and his Dad. Safe and returned to him, against all odds he had made it in time and saved them from that hellish place. For that matter, against all odds he had been able to cure them of the plague that was ravaging their bodies. That had been Rachel's doing, an immense accomplishment she had achieved against almost impossible odds too.

It killed him that she was now feeling like she had failed so dismally…after what she had really done was succeed so overwhelmingly. Succeed in doing something that the entire rest of the world had failed at completely.

For himself, he just kept thinking that maybe if he had done something…anything, just a little bit quicker, just a little bit different…he would have been able to save Darien too. But he knew better really, he knew doing anything different was infinitely more likely to have resulted in more loss…more death…not less. Probably with them not even making it to Baltimore with the Cure to start with, because Ruskov had blown them out of the water at any one of the numerous times that had been a distinct possibility.

No, he had personally beaten the odds to get his children and his father…and for that matter, Rachel as well, back with him. It was terrible to think, but he had gotten most of the people who meant the most to him back…saved them from this plague and the numerous other dangers that lurked around it. He had to be thankful for that…he _was_ thankful for that.

Darien would always hold a special place in his heart…he would always love her...nothing would change that. But after six months without seeing her, spending the last month of that preparing for the very real possibility that he had lost her…lost everyone, he knows her loss does not feel as sharp and fresh as it would have had the circumstances been different.

Tom knew exactly where his focus had to lie in the future…_on the future_. His children were his future…the continuation of their mission to save the world was his future…and the woman before him was his future. It might be too soon to admit it, but there it was.

"Rachel." He spoke her name gently to gain her attention back from the far off place it seemed to currently be residing.

"Hmm…" She looked at him, and after a couple of seconds her eyes came back to focus on him too. "Oh…I'm sorry, Captain. I was miles away."

"Tom."

"Sorry?"

"My name."

She understood then, she offered him a weak smile and spoke her acquiesce. "Tom."

He smiled too…also rather weakly.

"I know we haven't had much of a chance to talk since…well…" He let the sentence hang there; he didn't need to say since when…they both bloody well knew since when. He attempted to start over.

"I wanted us to have some to time alone, there hasn't been much of an opportunity until now but I think there are quite a few things we need to talk about."

She was silent for a long moment, considering his words…considering her words…he wasn't sure. When enough time had passed that he was almost sure the proverbial conversation ball had been passed back to him unused…she spoke…her voice soft.

"I'm sorry."

The random and, he was sure, unwarranted apology confused him.

"What possibly for?"

"Your wife…"

Tom understood her demeanor then.

"I appreciate and accept the condolence, but you have nothing to actually _be sorry_ for." And he very much suspected that had been what she actually meant. This woman collected guilt and responsibility like some people collected baseball cards.

"That's kind of you to say but we both know it's not true, Cap…Tom...I…"

He interrupted her then. "Is that what _we know_? I don't think so, Rachel. I'll tell you what _I know_. In a world where most of our population is already dead, and the rest are waiting to die by this plague…my father and my children were saved right out from its clutches. They are healthy and safe now, and amongst the first of the lucky few who will _not_ meet their end by this plague. That was your doing Rachel, and you and no one else could do it, we know that because everyone else tried and everyone else failed…_you_ achieved what the world believed impossible."

Rachel was silent for a long time, still eyeing him sorrowfully.

"But I was the one that stopped you form going to her sooner…"

"And what could I reasonably have done if I had gone for my family sooner, Rachel? My return to them was all but useless without bringing with me the means to beat this sickness…and only you could give me that… Your actions _saved_ my family…those that could be saved... no blame for anything else lies on your shoulders."

He studied her as she studied him…eventually she nodded, eyes downcast, indicating that she would accept his words. But he wondered, and worried, if she really truly did. A moment's more silence lasted before she spoke again.

"Your children are wonderful, Tom" Apparently she had decided to take the conversation in a happier direction. He wasn't about to argue, with either the new topic direction or her very true sentiments.

"They are." He agreed proudly, smiling. She returned the gesture with a sweet smile of her own, her eyes holding more happiness than sadness for at least a moment.

"Your father is a character." She continued.

Tom couldn't help but chuckle at that. In one line and one look he could tell she had his old man pegged. He had noticed that his father had taken quite a shine to Rachel…he supposed it was easy enough to see why he would…even if she hadn't saved his life…which of course she had.

Truthfully, between him being kept ruthlessly occupied supervising repairs to the ship after their _eventful _departure from Baltimore Harbor…and her spending most of her time caring for and watching over the sick and injured after their departure…Rachel had spent infinitely more time with his family then he had since they had come on board a week ago. A situation he greatly bemoaned, but was regretfully unavoidable. Obviously it was not Rachel's presence around his family that he had any objection too, quite the to contrary, it was his lack of ability to join them…_all of them_.

Of course neither his father nor his children needed her constant medical care now. Within days she had pronounced them completely healthy, much to his relief, but she had continued to hover over them like a mother hen nonetheless…none of them had not complained at her continued presence and attention…quite the opposite.

"He likes you…they all do." He had been present enough to clearly see that.

"I like them too." And he had pleasantly made that observance as well. It made his heart swell…seeing them together…all of them enjoying each other's company. It just seemed so_ right_.

He was sure they shared a moment then, sure both of them felt it, their gazes drawn together, smiles of their faces, silent but contentedly so. He could have happily kept up that moment forever…but Rachel broke it first, an almost self-conscious look on her beautiful features.

"You said there were things we needed to talk about." She prompted. Directing the conversation away from more personal directions he thought she could also feel that it was heading. Of course he worried about her reasons for wanting to direct their encounter away from such a direction. Was she just embarrassed? Self-conscious? _Uninterested_? He valiantly fought to ignore the last option.

Of course with her change of topic she was making the assumption that the business he had to discuss with her was _not_ of a personal nature… And thus she was going to be disappointed…_or not_…

"I think we need to return to the conversation we started after the trials….the one I cut short."

She was silent a long moment…wide eyes blinking at him not unlike an owl's.

"You mean…?" She spoke hesitantly, brow furrowed.

"Yes." He responded definitively. He could see that their roles had practically been reverses since they last spoke. But now having long considered her words and their current situation…he knew he needed to own the decision he had come to.

"I'm surprised you're bringing this up, you seemed…_very uncomfortable_…with the topic when last we spoke."

"I didn't say I still wasn't, but I can and will get over that, and I did say I would think on it, and I have been. Frankly, I'm surprised you haven't brought the topic back up before now…I can't imagine your estimations of the situation have improved after Baltimore and the set backs we now face?"

She was quiet for a long moment; he watched as her hardly joyous features fell even further into a look of deep resigned depression.

"No…no they have not…"

"How bad?"

"Real bad…almost bad enough to make the argument completely moot anyway."

"How could it…" He spoke before allowing all the cogs in his brain to properly fit into their assigned places…and then he got it. She was saying they could already be too late. Repopulation a moot point… little chance of the human race surviving regardless…

Well that was_ not_ going to work for him. He would not let anyone give up on his watch… He would not let _her _give up on his watch.

"You said _almost _bad enough…"

"Well, we don't have the exact situation on the ground…the exact numbers of people who are left…but…"

"But?" He prompted.

"But I think you'll agree the indications we are in possession of are pretty damn bad… Nuclear bombs being employed killing millions…_at least_…poisoning the land… Millions more deliberately and systematically murdered in the name of bringing to fruition ethically heinous agendas… Oh, and then there's the billions already gone due to the virus itself…which let's not forget was made so much worse by epic human stupidity to start with."

She still felt resolute disgust when she thought of her Norwegian counterpart, the man had killed so many with his selfish reckless arrogance and outright stupidity. There was more blood on his hands than the people who had bushed the red buttons on nuclear weapons…more so than any one person in human history actually…. hardly a distinction to elate in.

Tom could tell that even thinking about Ruskov's scientist still angered her greatly…apparently more so than Ruskov himself. But Tom thought he understood, the man had been responsible for the deaths of so very many and he had been one of her own… a colleague of sorts. That was probably why it was so personnel for her….aside form the fact he had had her hunted, of course…he was like her, a doctor, supposed to be dedicated to saving lives and his reckless arrogance had instead caused him to be responsible for the death of billions. It only added insult to a rather mammoth injury, that man had not even been remotely remorseful for his actions when Rachel had questioned him. His attention returned to the current as she continued.

"And here we are! With not only a vaccine, but a cure. What should have been _by far_ the biggest challenge successfully completed, and what have we got now? Massive road blocks being thrust up in our faces every time we are remotely close to finding a way to mass produce and disseminate it…and all of this is happening against a very fast ticking clock…"

She looked deeply depressed at her own words, he could absolutely understand it…but he couldn't allow her to wallow in it.

"Rachel, I know things seem bleak and hopeless right now, but you can't give up hope, I won't let you!"

She gave him a kind but sympathetic smile. He read it as '_poor fool still holds out hope_'. Damn, she really was in a funk. Well it didn't matter, by the end of this she was going to be just as foolishly optimistic as him…even if it killed him.

"Tom, none of the information we do have about the current global situation bodes remotely well for maintaining the hope that the truth lies on the optimistic side of predictions…quite the opposite actually. Trust me, the more pessimistic…and frankly realistic approximations of what could be our true current reality outside this ship… for lack of more eloquent way to say it…_truly suck_. So yeah, I am feeling less than optimistic right now…less than hopeful. And one needs to have at least some hope to argue the course of action I was arguing before…especially against such strong resistance."

She finished her speech on a mild note, but he could tell that he had initially hurt her by not being seen to give her words and warnings more credence. And in that case he was just as responsible for her giving up, if a good part of the reason she was, was because she simply didn't think she would get any support from the main person she needed support from.

"And if I've stopped resisting?"

Wide eyes…suddenly with more light in them…swung to meet him.

"Have you?" She asked hesitantly…

He would swear there _was_ in fact some remaining hope left in her…he could hear it in those two softly spoken words. Yes, she was feeling overwhelmed and depressed due to their current predicament…their losses…their disappointments, her scientific mind providing her with an unfortunately unrelentingly clear picture of how bad it could truly be…but she hadn't given up hope… The woman he had come to know so well never gave up…never.

Tom had already made up his mind, but in that moment, he wondered if he would have given an affirmative answer anyway just to see that look of hope on her face bloom…as it was doing right now gazing at his…apparently she did not need to listen to his words to read them in his face. He spoke them anyway.

"Yes, I have."

TBC

A/N: Thank you all for reading and for all the lovely reviews/follows/favorites. They always put a smile on my face.


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